Fig. 4. Phylogeny of Basidiomycota pheromone receptor proteins.

Amino acid sequences identified by BLAST from publically available databases or from genome projects were retrieved for representative species of the tree subphyla of the Basidiomycota. A total of 106 sequences were manually inspected, amended where necessary, aligned with MAFFT (195) and poorly aligned regions were trimmed with trimAl (196). The phylogenetic tree and branch support were obtained as in Fig. 2 and the tree was rooted with Saccharomyces cerevisiae Ste3p. GenBank accession numbers (∗), JGI protein identifiers (**) and RIKEN/NBRP identifiers (***) and are given after the strain name, with letters in superscript indicating: (a) genomes assembled from available raw sequencing data and inspected locally; (b) genomic contigs/scaffolds lacking gene annotation; (c) genes whose annotation was corrected. Species highlighted in boldface are shown in Fig. 3, with arrows before their names indicating the allelic version (or paralog) of the pheromone receptor as colored in Fig. 3. Of note, the STE3.1 and STE3.2 alleles in the Microbotryomycetes (Pucciniomycotina) displayed the deepest allelic divergence and trans-specific polymorphism, with the STE3.1 alleles of the different species branching together rather than each of these alleles clustering with the STE3.2 allele from the same species (42, 45, 137).